Merge master into main

3 files changed, 63 insertions, 0 deletions

diff --git a/files/data_io/transforms/__init__.py b/files/data_io/transforms/__init__.py
new file mode 100644
index 0000000..f6aa496
--- /dev/null
+++ b/files/data_io/transforms/__init__.py
@@ -0,0 +1 @@
+"""Transforms for spike data (normalization, augmentation, etc.)."""
diff --git a/files/data_io/transforms/normalization.py b/files/data_io/transforms/normalization.py
new file mode 100644
index 0000000..c86b8c7
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+++ b/files/data_io/transforms/normalization.py
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+import torch
+
+class Normalize:
+    """Normalize spike input (z-score or min-max)."""
+    def __init__(self, mode: str = "zscore", eps: float = 1e-6):
+        """
+        Parameters
+        ----------
+        mode : str
+            One of {"zscore", "minmax"}.
+            - "zscore": per-sample, per-channel standardization across time.
+            - "minmax": per-sample, per-channel min-max scaling across time.
+        eps : float
+            Small constant to avoid division by zero.
+        """
+        mode_l = str(mode).lower()
+        if mode_l not in {"zscore", "minmax"}:
+            raise ValueError(f"Normalize mode must be 'zscore' or 'minmax', got {mode}")
+        self.mode = mode_l
+        self.eps = float(eps)
+
+    def __call__(self, x: torch.Tensor) -> torch.Tensor:
+        """
+        Apply normalization.
+        Accepts tensors of shape (T, D) or (B, T, D).
+        Normalization is computed per-sample and per-channel over the time axis T.
+        """
+        if not isinstance(x, torch.Tensor):
+            raise TypeError("Normalize expects a torch.Tensor")
+        if x.ndim == 2:
+            # (T, D) -> time dim = 0
+            time_dim = 0
+            keep_dims = True
+        elif x.ndim == 3:
+            # (B, T, D) -> time dim = 1
+            time_dim = 1
+            keep_dims = True
+        else:
+            raise ValueError(f"Expected x.ndim in {{2,3}}, got {x.ndim}")
+
+        if self.mode == "zscore":
+            mean_t = x.mean(dim=time_dim, keepdim=keep_dims)
+            # population std (unbiased=False) to avoid NaNs for small T
+            std_t = x.std(dim=time_dim, keepdim=keep_dims, unbiased=False)
+            x_norm = (x - mean_t) / (std_t + self.eps)
+            return x_norm
+        else:  # "minmax"
+            min_t = x.amin(dim=time_dim, keepdim=keep_dims)
+            max_t = x.amax(dim=time_dim, keepdim=keep_dims)
+            denom = (max_t - min_t).clamp_min(self.eps)
+            x_scaled = (x - min_t) / denom
+            return x_scaled
diff --git a/files/data_io/transforms/spike_augmentation.py b/files/data_io/transforms/spike_augmentation.py
new file mode 100644
index 0000000..9b7b687
--- /dev/null
+++ b/files/data_io/transforms/spike_augmentation.py
@@ -0,0 +1,10 @@
+import torch
+
+class SpikeJitter:
+    """Add temporal jitter noise to spikes."""
+    def __init__(self, std=0.01):
+        self.std = std
+
+    def __call__(self, spikes: torch.Tensor) -> torch.Tensor:
+        # TODO: add random jitter to spike timings
+        return spikes